High-depth spatial transcriptome analysis by photo-isolation chemistry

Mizuki Honda, Shinya Oki (), Ryuichi Kimura, Akihito Harada, Kazumitsu Maehara, Kaori Tanaka, Chikara Meno and Yasuyuki Ohkawa ()
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Mizuki Honda: Graduate School of Medical Sciences, Kyushu University
Shinya Oki: Graduate School of Medical Sciences, Kyushu University
Ryuichi Kimura: Kyoto University Graduate School of Medicine
Akihito Harada: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University
Kazumitsu Maehara: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University
Kaori Tanaka: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University
Chikara Meno: Graduate School of Medical Sciences, Kyushu University
Yasuyuki Ohkawa: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions.

Date: 2021
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DOI: 10.1038/s41467-021-24691-8

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